Starting phenix.real_space_refine on Tue Mar 3 21:09:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wb2_21585/03_2026/6wb2_21585.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wb2_21585/03_2026/6wb2_21585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wb2_21585/03_2026/6wb2_21585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wb2_21585/03_2026/6wb2_21585.map" model { file = "/net/cci-nas-00/data/ceres_data/6wb2_21585/03_2026/6wb2_21585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wb2_21585/03_2026/6wb2_21585.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 9 5.16 5 C 5150 2.51 5 N 1465 2.21 5 O 1711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8407 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 705 Classifications: {'RNA': 33} Modifications used: {'5*END': 1, 'rna3p_pur': 19, 'rna3p_pyr': 13} Link IDs: {'rna3p': 32} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 880 Inner-chain residues flagged as termini: ['pdbres=" G D 46 "'] Classifications: {'DNA': 4, 'RNA': 38} Modifications used: {'5*END': 2, 'rna3p_pur': 15, 'rna3p_pyr': 21} Link IDs: {'rna3p': 41} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 3854 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 504} Chain breaks: 3 Unresolved non-hydrogen bonds: 543 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 429 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLU:plan': 33, 'PHE:plan': 2, 'ASP:plan': 10, 'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 8, 'ARG:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 287 Chain: "B" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 2968 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 30, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 29, 'ASP:plan': 12, 'GLN:plan1': 7, 'TYR:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 210 Time building chain proxies: 2.04, per 1000 atoms: 0.24 Number of scatterers: 8407 At special positions: 0 Unit cell: (100.7, 97.52, 119.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 P 72 15.00 O 1711 8.00 N 1465 7.00 C 5150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 285.4 milliseconds 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 38.7% alpha, 11.4% beta 37 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.787A pdb=" N LEU A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 45 " --> pdb=" O MET A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.684A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.643A pdb=" N LEU A 100 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.666A pdb=" N PHE A 116 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 118 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.749A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 253 through 269 removed outlier: 3.533A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 283 Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 404 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.534A pdb=" N ASP A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 removed outlier: 3.582A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 removed outlier: 3.763A pdb=" N ASN A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.695A pdb=" N ALA B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 removed outlier: 6.140A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.557A pdb=" N LYS B 103 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 121 through 128 removed outlier: 4.657A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.775A pdb=" N ASN B 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 173 removed outlier: 3.720A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 211 Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 278 through 283 removed outlier: 4.001A pdb=" N LEU B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 278 through 283' Processing helix chain 'B' and resid 296 through 311 Processing helix chain 'B' and resid 364 through 383 removed outlier: 3.979A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.513A pdb=" N TRP B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 3.620A pdb=" N ARG A 72 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 107 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 351 removed outlier: 7.312A pdb=" N LYS A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 343 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 329 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.556A pdb=" N THR A 362 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 454 through 455 Processing sheet with id=AA8, first strand: chain 'A' and resid 492 through 497 removed outlier: 4.133A pdb=" N VAL A 493 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 532 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A 497 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 62 removed outlier: 3.710A pdb=" N PHE B 61 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 74 " --> pdb=" O PHE B 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 179 through 181 removed outlier: 3.586A pdb=" N VAL B 189 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR B 107 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 131 through 132 removed outlier: 3.797A pdb=" N ILE B 132 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 142 " --> pdb=" O ILE B 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 347 through 354 removed outlier: 7.378A pdb=" N LYS B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN B 343 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 341 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N THR B 351 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYR B 339 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LYS B 353 " --> pdb=" O TRP B 337 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TRP B 337 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 390 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 97 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2109 1.33 - 1.45: 2037 1.45 - 1.57: 4484 1.57 - 1.69: 143 1.69 - 1.80: 16 Bond restraints: 8789 Sorted by residual: bond pdb=" CA VAL A 536 " pdb=" CB VAL A 536 " ideal model delta sigma weight residual 1.537 1.549 -0.012 1.29e-02 6.01e+03 8.63e-01 bond pdb=" CA VAL A 536 " pdb=" C VAL A 536 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.05e-02 9.07e+03 5.93e-01 bond pdb=" C GLU A 432 " pdb=" N PRO A 433 " ideal model delta sigma weight residual 1.331 1.339 -0.008 1.21e-02 6.83e+03 3.88e-01 bond pdb=" CA GLU B 169 " pdb=" C GLU B 169 " ideal model delta sigma weight residual 1.520 1.528 -0.007 1.23e-02 6.61e+03 3.44e-01 bond pdb=" CA THR A 386 " pdb=" CB THR A 386 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.55e-02 4.16e+03 3.41e-01 ... (remaining 8784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 12252 1.62 - 3.25: 142 3.25 - 4.87: 9 4.87 - 6.49: 3 6.49 - 8.12: 1 Bond angle restraints: 12407 Sorted by residual: angle pdb=" CA LEU A 525 " pdb=" CB LEU A 525 " pdb=" CG LEU A 525 " ideal model delta sigma weight residual 116.30 124.42 -8.12 3.50e+00 8.16e-02 5.38e+00 angle pdb=" CA VAL B 35 " pdb=" CB VAL B 35 " pdb=" CG2 VAL B 35 " ideal model delta sigma weight residual 110.40 113.21 -2.81 1.70e+00 3.46e-01 2.72e+00 angle pdb=" C ILE A 37 " pdb=" N CYS A 38 " pdb=" CA CYS A 38 " ideal model delta sigma weight residual 120.31 117.97 2.34 1.52e+00 4.33e-01 2.36e+00 angle pdb=" CA LEU A 260 " pdb=" CB LEU A 260 " pdb=" CG LEU A 260 " ideal model delta sigma weight residual 116.30 121.67 -5.37 3.50e+00 8.16e-02 2.35e+00 angle pdb=" N PRO A 4 " pdb=" CA PRO A 4 " pdb=" C PRO A 4 " ideal model delta sigma weight residual 114.68 113.09 1.59 1.04e+00 9.25e-01 2.32e+00 ... (remaining 12402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 4701 16.57 - 33.13: 297 33.13 - 49.70: 103 49.70 - 66.26: 102 66.26 - 82.83: 27 Dihedral angle restraints: 5230 sinusoidal: 2476 harmonic: 2754 Sorted by residual: dihedral pdb=" O5' C D 68 " pdb=" C5' C D 68 " pdb=" C4' C D 68 " pdb=" C3' C D 68 " ideal model delta sinusoidal sigma weight residual 175.00 117.96 57.04 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" O5' C D 61 " pdb=" C5' C D 61 " pdb=" C4' C D 61 " pdb=" C3' C D 61 " ideal model delta sinusoidal sigma weight residual 55.00 111.70 -56.70 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CB LYS B 70 " pdb=" CG LYS B 70 " pdb=" CD LYS B 70 " pdb=" CE LYS B 70 " ideal model delta sinusoidal sigma weight residual 60.00 112.90 -52.90 3 1.50e+01 4.44e-03 9.16e+00 ... (remaining 5227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1011 0.028 - 0.056: 282 0.056 - 0.084: 88 0.084 - 0.112: 69 0.112 - 0.141: 21 Chirality restraints: 1471 Sorted by residual: chirality pdb=" CA VAL A 536 " pdb=" N VAL A 536 " pdb=" C VAL A 536 " pdb=" CB VAL A 536 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE A 63 " pdb=" N ILE A 63 " pdb=" C ILE A 63 " pdb=" CB ILE A 63 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE A 50 " pdb=" N ILE A 50 " pdb=" C ILE A 50 " pdb=" CB ILE A 50 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 1468 not shown) Planarity restraints: 1302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 278 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C GLN A 278 " 0.038 2.00e-02 2.50e+03 pdb=" O GLN A 278 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 279 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 51 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A 52 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 94 " -0.022 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 95 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.019 5.00e-02 4.00e+02 ... (remaining 1299 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2438 2.81 - 3.34: 7343 3.34 - 3.86: 14475 3.86 - 4.38: 15217 4.38 - 4.90: 24135 Nonbonded interactions: 63608 Sorted by model distance: nonbonded pdb=" OG1 THR A 58 " pdb=" O ALA A 129 " model vdw 2.293 3.040 nonbonded pdb=" OG1 THR A 240 " pdb=" O VAL A 314 " model vdw 2.306 3.040 nonbonded pdb=" O GLY A 543 " pdb=" NE2 GLN A 547 " model vdw 2.324 3.120 nonbonded pdb=" OD2 ASP A 320 " pdb=" OG SER A 322 " model vdw 2.326 3.040 nonbonded pdb=" OD1 ASN A 460 " pdb=" N LYS A 461 " model vdw 2.366 3.120 ... (remaining 63603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.000 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8789 Z= 0.083 Angle : 0.443 8.118 12407 Z= 0.224 Chirality : 0.037 0.141 1471 Planarity : 0.004 0.037 1302 Dihedral : 16.508 82.830 3450 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.17 % Allowed : 4.59 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.23), residues: 932 helix: -1.60 (0.25), residues: 325 sheet: -2.38 (0.46), residues: 104 loop : -3.00 (0.23), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 199 TYR 0.003 0.000 TYR B 115 PHE 0.005 0.000 PHE A 77 TRP 0.012 0.000 TRP A 402 HIS 0.001 0.000 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00160 ( 8789) covalent geometry : angle 0.44314 (12407) hydrogen bonds : bond 0.15318 ( 374) hydrogen bonds : angle 5.71305 ( 948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8526 (tp30) REVERT: A 399 GLU cc_start: 0.8630 (pp20) cc_final: 0.8363 (tm-30) REVERT: B 24 TRP cc_start: 0.6859 (p90) cc_final: 0.6536 (p90) REVERT: B 31 ILE cc_start: 0.9566 (mt) cc_final: 0.9311 (tp) REVERT: B 116 PHE cc_start: 0.8193 (m-10) cc_final: 0.7976 (m-10) REVERT: B 149 LEU cc_start: 0.8714 (mm) cc_final: 0.8326 (mt) REVERT: B 153 TRP cc_start: 0.8522 (t60) cc_final: 0.8155 (t60) REVERT: B 373 GLN cc_start: 0.9130 (mt0) cc_final: 0.8616 (tm-30) REVERT: B 378 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8132 (mt-10) outliers start: 1 outliers final: 1 residues processed: 106 average time/residue: 0.1146 time to fit residues: 15.7486 Evaluate side-chains 66 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 151 GLN A 174 GLN A 367 GLN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN A 494 ASN A 547 GLN B 57 ASN B 367 GLN B 373 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.062243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.050413 restraints weight = 57944.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.051700 restraints weight = 33712.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.052607 restraints weight = 23079.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.053262 restraints weight = 17518.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.053702 restraints weight = 14247.588| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8789 Z= 0.112 Angle : 0.487 5.695 12407 Z= 0.244 Chirality : 0.039 0.159 1471 Planarity : 0.005 0.073 1302 Dihedral : 17.441 76.074 2139 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.27), residues: 932 helix: 0.12 (0.30), residues: 325 sheet: -1.72 (0.46), residues: 107 loop : -2.49 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 78 TYR 0.020 0.001 TYR A 441 PHE 0.023 0.002 PHE B 171 TRP 0.012 0.001 TRP A 402 HIS 0.014 0.002 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8789) covalent geometry : angle 0.48729 (12407) hydrogen bonds : bond 0.03327 ( 374) hydrogen bonds : angle 4.31203 ( 948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9300 (mm-30) cc_final: 0.8979 (tp30) REVERT: A 396 GLU cc_start: 0.9232 (pm20) cc_final: 0.8582 (pm20) REVERT: A 520 GLN cc_start: 0.9439 (pt0) cc_final: 0.9178 (pp30) REVERT: B 149 LEU cc_start: 0.8969 (mm) cc_final: 0.8699 (mm) REVERT: B 153 TRP cc_start: 0.8853 (t60) cc_final: 0.8155 (t60) REVERT: B 373 GLN cc_start: 0.9089 (mt0) cc_final: 0.8543 (tm-30) REVERT: B 378 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8240 (mt-10) REVERT: B 401 TRP cc_start: 0.8675 (m100) cc_final: 0.8433 (m100) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0910 time to fit residues: 9.6399 Evaluate side-chains 57 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 2 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.058665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.046901 restraints weight = 58006.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.048071 restraints weight = 34098.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.048893 restraints weight = 23512.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.049479 restraints weight = 17964.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.049899 restraints weight = 14749.138| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8789 Z= 0.163 Angle : 0.538 8.527 12407 Z= 0.271 Chirality : 0.039 0.158 1471 Planarity : 0.004 0.050 1302 Dihedral : 17.633 78.525 2139 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.17 % Allowed : 5.95 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.27), residues: 932 helix: 0.76 (0.31), residues: 322 sheet: -1.54 (0.47), residues: 109 loop : -2.30 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 78 TYR 0.014 0.001 TYR B 354 PHE 0.009 0.001 PHE A 227 TRP 0.016 0.002 TRP A 398 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8789) covalent geometry : angle 0.53825 (12407) hydrogen bonds : bond 0.03833 ( 374) hydrogen bonds : angle 4.24244 ( 948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.9254 (t0) cc_final: 0.9053 (t0) REVERT: A 300 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8398 (tm-30) REVERT: A 370 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8739 (tp30) REVERT: B 367 GLN cc_start: 0.9054 (pt0) cc_final: 0.8642 (pm20) REVERT: B 373 GLN cc_start: 0.9242 (mt0) cc_final: 0.8689 (tm-30) outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.0789 time to fit residues: 6.4460 Evaluate side-chains 39 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 72 optimal weight: 0.2980 chunk 38 optimal weight: 8.9990 chunk 48 optimal weight: 0.0040 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.058965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.047160 restraints weight = 58618.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.048387 restraints weight = 33651.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.049264 restraints weight = 22920.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.049849 restraints weight = 17348.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.050294 restraints weight = 14215.043| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8789 Z= 0.107 Angle : 0.479 6.362 12407 Z= 0.238 Chirality : 0.038 0.160 1471 Planarity : 0.004 0.045 1302 Dihedral : 17.623 79.644 2139 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.28), residues: 932 helix: 1.10 (0.31), residues: 328 sheet: -1.34 (0.47), residues: 109 loop : -2.15 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 78 TYR 0.011 0.001 TYR B 115 PHE 0.021 0.001 PHE B 160 TRP 0.016 0.001 TRP B 414 HIS 0.006 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8789) covalent geometry : angle 0.47928 (12407) hydrogen bonds : bond 0.03207 ( 374) hydrogen bonds : angle 3.98857 ( 948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.9256 (t0) cc_final: 0.9036 (t0) REVERT: A 370 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8780 (tp30) REVERT: A 399 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8613 (tm-30) REVERT: B 153 TRP cc_start: 0.9013 (t60) cc_final: 0.8167 (t60) REVERT: B 367 GLN cc_start: 0.9028 (pt0) cc_final: 0.8584 (pm20) REVERT: B 373 GLN cc_start: 0.9255 (mt0) cc_final: 0.8574 (tm-30) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0803 time to fit residues: 7.2459 Evaluate side-chains 42 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.059293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.047533 restraints weight = 56642.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.048771 restraints weight = 32760.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.049650 restraints weight = 22327.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.050274 restraints weight = 16867.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.050694 restraints weight = 13671.875| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8789 Z= 0.087 Angle : 0.458 5.645 12407 Z= 0.226 Chirality : 0.038 0.140 1471 Planarity : 0.004 0.042 1302 Dihedral : 17.579 79.716 2139 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.28), residues: 932 helix: 1.25 (0.31), residues: 329 sheet: -1.14 (0.48), residues: 109 loop : -1.95 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.010 0.001 TYR A 188 PHE 0.007 0.001 PHE A 130 TRP 0.015 0.001 TRP A 229 HIS 0.005 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00190 ( 8789) covalent geometry : angle 0.45816 (12407) hydrogen bonds : bond 0.02941 ( 374) hydrogen bonds : angle 3.81993 ( 948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.9236 (t0) cc_final: 0.9013 (t0) REVERT: B 149 LEU cc_start: 0.8887 (mm) cc_final: 0.8578 (mm) REVERT: B 153 TRP cc_start: 0.8999 (t60) cc_final: 0.8046 (t60) REVERT: B 171 PHE cc_start: 0.8384 (p90) cc_final: 0.7972 (p90) REVERT: B 367 GLN cc_start: 0.9010 (pt0) cc_final: 0.8566 (pm20) REVERT: B 373 GLN cc_start: 0.9139 (tt0) cc_final: 0.8561 (tm-30) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0804 time to fit residues: 6.7191 Evaluate side-chains 45 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 0.0040 chunk 49 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.058881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.047121 restraints weight = 56491.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.048358 restraints weight = 32860.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.049229 restraints weight = 22471.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.049844 restraints weight = 17038.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.050270 restraints weight = 13899.243| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8789 Z= 0.097 Angle : 0.466 5.568 12407 Z= 0.231 Chirality : 0.038 0.140 1471 Planarity : 0.004 0.043 1302 Dihedral : 17.604 79.546 2139 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.17 % Allowed : 2.55 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.28), residues: 932 helix: 1.46 (0.31), residues: 329 sheet: -0.99 (0.49), residues: 109 loop : -1.80 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.021 0.001 TYR A 183 PHE 0.019 0.001 PHE B 160 TRP 0.013 0.001 TRP A 402 HIS 0.005 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 8789) covalent geometry : angle 0.46628 (12407) hydrogen bonds : bond 0.03117 ( 374) hydrogen bonds : angle 3.77518 ( 948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 LEU cc_start: 0.8900 (mm) cc_final: 0.8595 (mm) REVERT: B 153 TRP cc_start: 0.9018 (t60) cc_final: 0.8018 (t60) REVERT: B 367 GLN cc_start: 0.9049 (pt0) cc_final: 0.8571 (pm20) REVERT: B 373 GLN cc_start: 0.9171 (tt0) cc_final: 0.8569 (tm-30) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.0801 time to fit residues: 6.8967 Evaluate side-chains 44 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 89 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.059001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.047226 restraints weight = 58415.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.048474 restraints weight = 33637.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.049339 restraints weight = 22912.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.049964 restraints weight = 17348.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.050390 restraints weight = 14131.576| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8789 Z= 0.090 Angle : 0.466 5.573 12407 Z= 0.233 Chirality : 0.038 0.172 1471 Planarity : 0.004 0.041 1302 Dihedral : 17.622 79.720 2139 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.17 % Allowed : 0.85 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.29), residues: 932 helix: 1.54 (0.32), residues: 322 sheet: -0.88 (0.49), residues: 109 loop : -1.63 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 206 TYR 0.018 0.001 TYR A 183 PHE 0.018 0.001 PHE B 171 TRP 0.013 0.001 TRP A 402 HIS 0.011 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 8789) covalent geometry : angle 0.46637 (12407) hydrogen bonds : bond 0.03089 ( 374) hydrogen bonds : angle 3.79013 ( 948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 LEU cc_start: 0.8893 (mm) cc_final: 0.8616 (mm) REVERT: B 153 TRP cc_start: 0.9006 (t60) cc_final: 0.8038 (t60) REVERT: B 367 GLN cc_start: 0.9054 (pt0) cc_final: 0.8595 (pm20) REVERT: B 373 GLN cc_start: 0.9137 (tt0) cc_final: 0.8536 (tm-30) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.0813 time to fit residues: 6.9686 Evaluate side-chains 43 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 85 GLN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.056403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.044802 restraints weight = 59212.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.045947 restraints weight = 34874.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.046756 restraints weight = 24176.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.047333 restraints weight = 18564.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.047748 restraints weight = 15283.116| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8789 Z= 0.154 Angle : 0.527 5.644 12407 Z= 0.265 Chirality : 0.039 0.163 1471 Planarity : 0.004 0.047 1302 Dihedral : 17.795 84.347 2139 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.17 % Allowed : 0.34 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.29), residues: 932 helix: 1.40 (0.31), residues: 328 sheet: -1.05 (0.47), residues: 111 loop : -1.65 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 143 TYR 0.014 0.001 TYR A 183 PHE 0.016 0.002 PHE B 160 TRP 0.020 0.002 TRP B 212 HIS 0.004 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8789) covalent geometry : angle 0.52686 (12407) hydrogen bonds : bond 0.04127 ( 374) hydrogen bonds : angle 4.05837 ( 948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.9478 (mmm) cc_final: 0.9213 (tpp) REVERT: B 40 GLU cc_start: 0.9105 (mp0) cc_final: 0.8898 (mp0) REVERT: B 208 HIS cc_start: 0.8848 (m90) cc_final: 0.8645 (m170) REVERT: B 367 GLN cc_start: 0.9143 (pt0) cc_final: 0.8647 (pm20) REVERT: B 373 GLN cc_start: 0.9178 (tt0) cc_final: 0.8587 (tm-30) outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.0860 time to fit residues: 6.6123 Evaluate side-chains 37 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 27 optimal weight: 0.0170 chunk 21 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 28 optimal weight: 0.0170 chunk 72 optimal weight: 0.9990 chunk 82 optimal weight: 0.0770 chunk 52 optimal weight: 0.0270 chunk 65 optimal weight: 4.9990 chunk 78 optimal weight: 0.0470 overall best weight: 0.0370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 520 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.058958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.047117 restraints weight = 57504.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.048365 restraints weight = 33397.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.049245 restraints weight = 22858.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.049865 restraints weight = 17359.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.050300 restraints weight = 14153.272| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8789 Z= 0.086 Angle : 0.472 5.557 12407 Z= 0.232 Chirality : 0.038 0.148 1471 Planarity : 0.004 0.038 1302 Dihedral : 17.569 80.075 2139 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.17 % Allowed : 0.68 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.29), residues: 932 helix: 1.63 (0.32), residues: 321 sheet: -0.53 (0.49), residues: 105 loop : -1.45 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 358 TYR 0.018 0.001 TYR A 183 PHE 0.026 0.001 PHE B 160 TRP 0.014 0.001 TRP A 402 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00182 ( 8789) covalent geometry : angle 0.47156 (12407) hydrogen bonds : bond 0.03038 ( 374) hydrogen bonds : angle 3.76739 ( 948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 LEU cc_start: 0.8877 (mm) cc_final: 0.8416 (mt) REVERT: B 153 TRP cc_start: 0.9038 (t60) cc_final: 0.7976 (t60) REVERT: B 367 GLN cc_start: 0.9057 (pt0) cc_final: 0.8492 (pm20) REVERT: B 373 GLN cc_start: 0.9119 (tt0) cc_final: 0.8649 (tm-30) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.0714 time to fit residues: 6.7616 Evaluate side-chains 47 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 67 optimal weight: 0.7980 chunk 11 optimal weight: 0.0570 chunk 43 optimal weight: 5.9990 chunk 15 optimal weight: 0.1980 chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 520 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.058667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.046814 restraints weight = 57798.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.048050 restraints weight = 33625.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.048933 restraints weight = 23088.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.049556 restraints weight = 17543.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.050003 restraints weight = 14276.731| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8789 Z= 0.081 Angle : 0.468 5.609 12407 Z= 0.231 Chirality : 0.038 0.157 1471 Planarity : 0.004 0.037 1302 Dihedral : 17.552 79.381 2139 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.29), residues: 932 helix: 1.77 (0.32), residues: 320 sheet: -0.43 (0.49), residues: 105 loop : -1.33 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.019 0.001 TYR A 183 PHE 0.027 0.001 PHE B 160 TRP 0.014 0.001 TRP A 402 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00180 ( 8789) covalent geometry : angle 0.46780 (12407) hydrogen bonds : bond 0.03101 ( 374) hydrogen bonds : angle 3.70474 ( 948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.9423 (mmm) cc_final: 0.8911 (tpp) REVERT: B 149 LEU cc_start: 0.8911 (mm) cc_final: 0.8468 (mt) REVERT: B 153 TRP cc_start: 0.9074 (t60) cc_final: 0.8038 (t60) REVERT: B 367 GLN cc_start: 0.9088 (pt0) cc_final: 0.8559 (pm20) REVERT: B 373 GLN cc_start: 0.9163 (tt0) cc_final: 0.8656 (tm-30) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 0.0765 time to fit residues: 6.7570 Evaluate side-chains 43 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 100 optimal weight: 0.1980 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 0.1980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 520 GLN B 208 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.058848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.046946 restraints weight = 56287.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.048211 restraints weight = 32513.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.049083 restraints weight = 22192.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.049703 restraints weight = 16839.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.050129 restraints weight = 13740.506| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8789 Z= 0.083 Angle : 0.468 6.827 12407 Z= 0.232 Chirality : 0.038 0.155 1471 Planarity : 0.004 0.036 1302 Dihedral : 17.545 79.362 2139 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.29), residues: 932 helix: 1.76 (0.32), residues: 320 sheet: -0.60 (0.46), residues: 120 loop : -1.27 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.019 0.001 TYR A 183 PHE 0.026 0.001 PHE B 160 TRP 0.019 0.001 TRP B 414 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00184 ( 8789) covalent geometry : angle 0.46767 (12407) hydrogen bonds : bond 0.03066 ( 374) hydrogen bonds : angle 3.69351 ( 948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1176.38 seconds wall clock time: 21 minutes 2.42 seconds (1262.42 seconds total)